Two minor, but annoying, problems with the new version in Debian 7.0 64 bit/
#1 The pull down menus in the graphics windows refuse to remain open when
clicked, unless I left click and hold. Is this normal behavior?
#2. Caver 2.1.2 will not save the location of the Directory with the
plug-in .jar file. The work around is rather cumbersome.

Hi Gary,
actually PyMOL should be optimized for red/cyan and not green/magenta.
There is no option to change the colors, sorry.
In PyMOL 1.5 anaglyph has been improved and there are is an
"anaglyph_mode" settings which defaults to 4 ("optimized anaglyph").
Other reasonable values are 3 ("half-color") and 1 (gray).
http://pymol.org/dsc/dokuwiki/doku.php?id=setting:anaglyph_mode
If you really need to change the colors, you could take the open-source
code and tweak the anaglyph_mode matrix in layer1/Scene.c
Hope that helps.
Cheers,
Thomas
Gary Hunter wrote, On 06/17/13 09:53:
> Is there a way to customise the colours used in anaglyph stereo mode?
> Anaglyph mode has been optimised for green/magenta glasses but I have
> lots of red/cyan ones so I'd like to change the colours used if I can.
> Gary
>
> Prof. Gary J. Hunter,
> Department of Physiology and Biochemistry
> University of Malta, Msida, MSD 2080, Malta.
> phone: +356 2340 2917
> phone: +356 21316655 (secretary), Fax: +356 21310577
> http://www.um.edu.mt/ms/physbiochem
--
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Dear Pymol Users,
I have been trying to configure APBS-1.4 plugin of pymol 1.6 on a Debian
Wheezy machine. The initialization is successful, but when I hit "set
grid", I got the error message below:
*error: 1
<type 'exceptions.UnboundLocalError'> Exception in Tk callback
Function: <function <lambda> at 0x33a6938> (type: <type 'function'>)
Args: ()
Traceback (innermost last):
File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line
1747, in __call__
return apply(self.func, args)
File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py",
line 153, in <lambda>
command=lambda self=self, name=name: self._doCommand(name))
File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py",
line 132, in _doCommand
return command(name)
File
"/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line
1075, in execute
self.runPsize()
File
"/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line
1096, in runPsize
good = self.generatePqrFile()
File
"/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line
1007, in generatePqrFile
good = self._generatePdb2pqrPqrFile()
File
"/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line
1615, in _generatePdb2pqrPqrFile
if retval != 0:
<type 'exceptions.UnboundLocalError'>: local variable 'retval' referenced
before assignment*
Also, although I specified the PATH of APBS and PDB2PQR in apbs_tools.py
file, the APBS GUI in pymol is still unable to show the correct path of
APBS and PDB2PQR.
Thank you so much!
Sincerely,
Chen